Having a single company mostly control an Open Source project means that if the company decides to drop the project, stop funding it, and/or move devs from working on it to work on something else, progress halts and it's difficult to get things back. That's why so many projects try to have Foundation that controls resources and can be financially backed, etc.

There's also the "if the company goes evil the project may also be affected", like Red Hat pulling the carpet under CentOS or many other examples.